free turbo tax for military not applying at checkout.

If you are E1-E9, it shouldn't charge you, as long as you meet the criteria below and haven't used LIVE or any other add-ons.   Here's how one would normally get the military discount.  Commonly military filers miss the Step 3 shown below.

To get the military discount you must do all of these:

1)  In the Personal Info (My Info) section, indicate you were in armed forces, then indicate "active duty", answer question about pay grade, and the rest of the military questions there.

2)  Enter a W-2 from DFAS

3)  On a screen after W-2, you will ultimately see a screen that ask something like "Let's check for uncommon situations" or "Does your W-2 have any of these uncommon situations?"  or words to that effect.  It shows maybe 10-11 things with check boxes.   Be sure to again indicate there that you are "active duty military."   I don't know why it asks twice, but it must be checked again there.

4)   If it still tries to charge you, we can tell you how to get help from TurboTax Customer Support.     It's much harder to resolve if you have already paid.